Sequence specific DNA binding small molecules that can permeate human cells could potentially regulate transcription of specific genes. In an era when the human genome has been mapped and sequenced and the fields of biology and human medicine have revealed that many human diseases are linked to aberrant gene expression, fundamental research in DNA binding ligands could lead to reagents for functional genomics and possibly a new class of human therapeutics. Our objective has been to elucidate chemical principles for the design of small molecules which bind predetermined DNA sequences with the affinity and specificity of transcription factors (TF). Polyamides can inhibit binding of TF in promoters, inhibit (and activate) specific gene expression in cell-free systems and bind condensed DNA, chromatin. Synthetic polyamides have been shown to inhibit viral gene expression in primary human T-cells, and to modulate gain (and loss) of phenotype in a complex organism (Drosophila). With regard to specific aims: (1) a new class of polyamides conjugated to transporter peptides for enhanced nuclear uptake will be explored to broaden the repertoire of cell types (human, yeast, Drosophila) which allow nuclear uptake, (2) artificial transcriptional activators comprised of polyamide linked to peptide activation domains will be studied in cell culture, (3) polyamides conjugated to HDAC inhibitors will be used to modulate transcription, (4) a new class of polyamide-intercalators will be used to elucidate the role of MEF2 transcription factor in the matrix associated region in interphase chromatin, (5) polyamides which inhibit retroviral integrase will be tested in cell culture, (6) polyamides will be used to study the host cell molecular mechanism that regulates HIV latency in resting CD4+ lymphocytes, (7) polyamides-chlorambucil conjugates will be used in NB4 human cells to target the PML promoter, and (8) polyamides will be used to control gene expression and development in living zebrafish embryos.